Thank you for your help the other day. I was able to create the covariate file using the pre-imputation files. Now, when I use this covariate file with the command: Rscript PRSice.R --prsice PRSice_linux --base xxx.gz --target yyy_Chr#.QC --binary-target T --pheno zzz.txt --pheno-col www --cov www.covariate --base-maf MAF:0.01 --base-info imputationInfo:0.8 --stat BETA --beta --snp SNPID --A1 Allele2 --A2 Allele1 --pvalue p.value --out yyy
I encounter the error: Error: Invalid .bed file size for yyy_Chr2.QC.bed.
When I changed the --target yyy_Chr#.QC part to --target yyy_Chr2.QC to process only chromosome 2, the analysis completed successfully. I also confirmed that there is no corruption in yyy_Chr2.QC.bed using the md5sum command. I am at a loss for what to do next and would greatly appreciate your guidance on how to resolve this issue. Thank you very much.
Thank you for your help the other day. I was able to create the covariate file using the pre-imputation files. Now, when I use this covariate file with the command: Rscript PRSice.R --prsice PRSice_linux --base xxx.gz --target yyy_Chr#.QC --binary-target T --pheno zzz.txt --pheno-col www --cov www.covariate --base-maf MAF:0.01 --base-info imputationInfo:0.8 --stat BETA --beta --snp SNPID --A1 Allele2 --A2 Allele1 --pvalue p.value --out yyy I encounter the error: Error: Invalid .bed file size for yyy_Chr2.QC.bed. When I changed the --target yyy_Chr#.QC part to --target yyy_Chr2.QC to process only chromosome 2, the analysis completed successfully. I also confirmed that there is no corruption in yyy_Chr2.QC.bed using the md5sum command. I am at a loss for what to do next and would greatly appreciate your guidance on how to resolve this issue. Thank you very much.